Contacts of the helix formed by residues 101 - 118 (chain B) in PDB entry 4OL0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B VAL* 3.7 29.9 - - - +
97B LEU 4.5 0.6 + - - -
98B LYS 5.0 1.1 - - - -
100B LEU* 1.3 83.8 - - - +
102B PRO* 1.3 77.4 - - - +
103B VAL* 3.1 20.1 + - - +
104B ILE* 3.1 16.8 + - - +
105B VAL* 3.4 12.9 + - - +
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Residues in contact with PRO 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU* 4.6 17.5 - - + +
98B LYS 5.5 0.4 - - - +
101B SER* 1.3 90.5 - - - +
103B VAL* 1.3 55.0 + - + +
104B ILE 3.3 0.2 - - - -
105B VAL* 3.3 13.4 + - + +
106B THR* 2.6 41.8 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 4.6 8.7 - - + -
110A ARG 4.6 4.0 - - - +
111A VAL* 3.2 33.7 - - + +
113A GLU* 6.1 4.0 - - + -
57B VAL* 4.5 7.6 - - + -
61B TYR* 3.9 27.4 - - + -
101B SER* 3.5 19.1 - - - +
102B PRO* 1.3 79.1 - - + +
104B ILE* 1.3 69.3 + - + +
106B THR* 3.2 8.8 + - - -
107B GLN* 2.9 33.6 + - - +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 4.9 0.4 - - + -
57B VAL* 3.7 19.7 - - + +
60B CYS* 3.5 32.8 - - + +
61B TYR* 3.9 17.9 - - - +
64B ALA* 4.3 4.7 - - + -
97B LEU* 3.7 28.0 - - + +
100B LEU* 3.6 28.3 - - + -
101B SER* 3.1 9.8 + - - +
103B VAL* 1.3 81.5 - - + +
105B VAL* 1.3 60.9 + - - +
107B GLN* 3.2 6.4 + - - +
108B LEU* 2.8 41.1 + - + +
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 3.8 9.3 - - + +
97B LEU 3.5 15.0 - - - +
98B LYS* 3.4 29.4 - - - +
101B SER 3.6 9.0 - - - +
102B PRO* 3.3 13.7 + - + +
104B ILE* 1.3 76.4 - - - +
106B THR* 1.3 52.7 + - - +
108B LEU* 3.4 8.0 + - + +
109B ALA* 2.8 32.6 + - - +
141B PRO 5.7 0.2 - - - -
142B PHE* 3.5 35.4 - - + -
145B GLU* 4.8 8.1 - - + -
200B LYS* 6.4 0.2 - - - +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 3.5 42.7 + - + +
102B PRO* 2.6 30.1 + - - +
103B VAL 3.3 6.7 - - - -
104B ILE 3.1 0.2 - - - -
105B VAL* 1.3 71.7 - - - +
107B GLN* 1.3 61.7 + - - +
109B ALA* 3.1 7.3 + - - +
110B LEU* 2.8 39.4 + - + +
145B GLU* 3.8 26.1 + - - +
149B VAL* 6.0 1.6 - - + -
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 4.0 8.1 + - - +
110A ARG* 5.0 4.8 + - - +
111A VAL* 3.9 15.6 - - - +
61B TYR* 3.5 32.8 + - + -
64B ALA* 3.6 22.9 - - + -
65B GLN* 3.4 28.0 - - + +
68B LYS* 3.3 29.1 + - - +
103B VAL 2.9 22.4 + - - +
104B ILE 3.7 0.7 - - - +
106B THR* 1.3 72.4 - - - +
108B LEU* 1.3 57.2 + - - +
110B LEU* 3.2 20.0 + - - +
111B ALA* 2.8 28.1 + - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 4.2 19.5 - - + -
64B ALA* 3.8 21.5 - - + +
67B MET* 5.5 1.1 - - + -
90B LEU* 4.7 18.1 - - + +
93B HIS* 4.0 15.0 - - + +
94B ILE* 3.6 41.5 - - + +
97B LEU* 4.6 6.7 - - + -
104B ILE* 2.8 34.7 + - + +
105B VAL* 3.8 4.7 - - - +
107B GLN* 1.3 73.0 - - - +
109B ALA* 1.3 60.6 + - - +
111B ALA* 3.2 6.1 + - + +
112B ILE* 2.9 36.0 + - - +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 4.0 4.0 - - + +
105B VAL 2.8 22.6 + - - +
106B THR 3.1 5.6 + - - +
108B LEU* 1.3 74.4 - - - +
110B LEU* 1.3 56.4 + - - +
112B ILE* 3.3 3.2 + - - +
113B ALA* 2.9 30.8 + - - +
145B GLU* 3.6 26.7 - - + +
146B ILE* 3.8 28.6 - - + +
149B VAL* 3.9 6.9 - - + +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 5.5 1.8 - - - +
110A ARG* 3.3 42.0 - - + +
68B LYS* 3.4 31.0 - - + +
106B THR* 2.8 23.4 + - + +
107B GLN* 3.4 26.2 - - - +
109B ALA* 1.3 76.5 - - - +
111B ALA* 1.3 56.4 + - - +
113B ALA* 3.4 0.5 + - - +
114B ASP* 2.8 35.7 + - - +
149B VAL* 3.3 26.2 - - + -
153B GLU* 3.5 17.9 - - + +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ALA 4.9 0.7 - - - +
67B MET* 4.6 5.2 - - + -
68B LYS* 3.7 24.8 - - - +
71B ILE* 2.8 31.3 - - + +
90B LEU* 3.6 21.5 - - + -
107B GLN 2.8 13.7 + - - +
108B LEU* 3.4 12.3 - - + +
110B LEU* 1.3 76.1 - - - +
112B ILE* 1.3 63.4 + - - +
115B LEU* 2.9 9.2 + - - +
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG* 5.7 5.6 - - + -
90B LEU* 3.7 28.0 - - + +
91B LEU* 3.8 27.1 - - + -
94B ILE* 4.0 24.9 - - + -
108B LEU 2.9 24.1 + - - +
109B ALA 3.6 4.3 - - - +
111B ALA* 1.3 71.7 - - - +
113B ALA* 1.3 59.4 + - - +
115B LEU* 3.3 4.8 + - - +
116B ALA* 2.8 28.9 + - + +
125B CYS* 6.5 0.4 - - - -
129B LEU* 4.5 12.3 - - + -
146B ILE* 3.8 37.0 - - + -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ALA 2.9 17.0 + - - +
110B LEU 3.7 3.1 - - - +
112B ILE* 1.3 77.2 - - - +
114B ASP* 1.3 60.6 + - - +
116B ALA* 2.9 10.9 + - - +
117B LEU* 2.8 33.7 + - - +
146B ILE* 4.8 6.5 - - + +
149B VAL* 3.6 24.7 - - + +
150B LEU* 4.0 21.8 - - + -
153B GLU* 4.8 2.0 - - + -
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Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LYS* 3.7 13.0 - - - +
71B ILE* 3.8 16.6 - - + -
72B GLN* 3.0 26.7 - - + +
110B LEU 2.8 23.8 + - - +
113B ALA* 1.3 72.5 - - - +
115B LEU* 1.3 61.4 + - - +
117B LEU* 3.6 7.9 + - - +
118B GLN* 2.9 36.1 + - - +
153B GLU* 2.8 40.7 - - - +
159B LEU* 3.8 10.5 - - + +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 3.5 11.8 - - + +
75B PHE* 3.8 28.7 - - + -
83B HIS* 5.1 3.1 - - + +
86B LEU* 3.7 39.5 - - + -
87B ARG* 3.9 25.8 - - + +
90B LEU* 4.4 7.0 - - + -
111B ALA 2.9 18.3 + - - +
112B ILE* 3.5 4.9 - - - +
114B ASP* 1.3 75.2 - - - +
116B ALA* 1.3 65.3 + - - +
118B GLN* 3.4 4.3 + - - -
119B MET* 3.4 44.1 + - + +
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ILE* 2.8 18.3 + - + +
113B ALA* 2.9 12.3 + - - +
115B LEU* 1.3 79.1 - - - +
117B LEU* 1.3 63.8 + - - +
118B GLN 3.3 0.5 + - - -
119B MET* 3.4 17.9 - - - +
123B LYS* 4.4 13.2 + - - +
125B CYS* 3.7 37.4 - - + -
129B LEU* 5.9 1.6 - - + -
150B LEU* 4.5 10.3 - - + -
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA 2.8 23.2 + - - +
114B ASP* 3.9 8.1 - - - +
115B LEU 3.3 0.2 - - - -
116B ALA* 1.3 74.8 - - - +
118B GLN* 1.3 59.4 + - + +
119B MET 3.5 2.1 + - - +
123B LYS* 5.1 12.6 + - - +
150B LEU* 3.8 25.1 - - + +
153B GLU* 3.7 42.4 - - + +
154B VAL* 4.1 12.1 - - + +
159B LEU* 4.8 9.9 - - + -
161B ILE* 4.4 3.8 - - + +
165B ARG* 5.6 1.6 + - - -
169B ILE* 4.0 47.4 - - + +
173B LEU* 5.3 3.4 - - + -
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE 3.1 26.4 + - - +
72B GLN* 4.5 7.0 + - - +
75B PHE* 3.2 49.5 - - + +
114B ASP* 2.9 24.4 - - - +
115B LEU* 3.4 4.9 + - - +
116B ALA 3.3 0.6 - - - -
117B LEU* 1.3 77.6 - - - +
119B MET* 1.3 57.3 + - - +
120B PRO* 4.4 3.9 - - - +
159B LEU* 3.4 21.2 - - - +
160B ARG* 5.5 9.0 + - - +
161B ILE* 3.6 27.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il